3 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
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16 * PURPOSE. See the GNU General Public License for more details.
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23 <title>Sequence Feature Settings Dialog Box</title>
27 <strong>Sequence Feature Settings Dialog Box</strong>
30 Select <strong>View→Feature Settings...</strong> menu entry in
31 an alignment window to open the feature settings dialog box, which
32 allows you to precisely control the presence and appearance of
33 sequence features for the current alignment.
36 <img src="featureSettings.gif" width="400" height="452"> <br>
37 Sequence Feature Settings for the Jalview Application</img>
40 The top section of the dialog box lists all the sequence feature
41 groups, along with a tickbox for each that controls whether its
42 features are displayed. The table in the middle lists all the
43 features in the currently selected groups, along with their display
44 style and whether they are currently being displayed (only the
45 ticked features and groups are displayed). <strong><em>You
46 can change the colour or shading style used for a feature in the
47 associated alignment by clicking on its colour box.</em></strong>
50 <a name="selectbyfeature"><strong><em>Selecting
51 alignment columns by feature</em></strong></a><br> <strong>Double-clicking
52 a feature type</strong> in the <strong>Feature Settings</strong> dialog
53 allows you to select columns in the alignment that contain (or do
54 not contain) features of that type. If a region of the alignment is
55 currently selected, then only features in the current selection will
56 be searched. The following keys affect the way in which selections
59 <li>Hold down <strong>Alt</strong> to select columns not
60 containing features of a particular type.
62 <li>Hold down <strong>Shift</strong> to add columns to the
65 <li>Press <strong>Command/Windows key</strong> to toggle column
69 Options are also provided in the feature's pop-up menu (see below).
71 <em>Select columns by feature was added in Jalview 2.8.1</em>
74 <strong><em>Feature settings pop-up menu</em></strong><br> <strong>Right-click</strong>
75 on a feature to open a pop-up menu that allows you to sort the
76 alignment or current selection using that feature type (see below),
77 or toggle the type of colouring used for the feature. Features may
78 be highlighted with either a single colour or a <a
79 href="featureschemes.html"
80 >feature colourscheme</a> based on either the scores associated with
81 that feature or from the feature's description (e.g. to distinguish
82 different names associated with a DOMAIN feature).
85 <strong>Ordering alignment by features</strong><br> The 'Seq
86 Sort by Score' and 'Seq Sort by Density' buttons will sort the
87 alignment based on the average score or total number of currently
88 active features and groups on each sequence. To order the alignment
89 using a specific feature type, use the <em>sort by ..</em> entries
90 in the pop-up menu for that type.<br> <em>Feature sorting
91 and graduated feature colouring were introduced in Jalview 2.5</em>
95 <strong>Transparency and Feature Ordering</strong>
97 <p>It is important to realise that sequence features are often not
98 distinct and often overlap (for example, a metal binding site
99 feature may be attached to one position along a stretch of sequence
100 marked with a secondary structure feature).</p>
102 The ordering of the sequence features in the dialog box list is the
103 order used by Jalview for rendering sequence features. A feature at
104 the bottom of the list is rendered <em>below</em> a feature higher
105 up in the list.<br> <em><strong>You can change
106 the order of a feature by dragging it up and down the list with
107 the mouse (not applet)</strong></em>.
110 The <strong><em>Optimise order</em></strong> button (currently only
111 available in the application) will re-order the feature render
112 ordering based on the average length of each feature type.
115 The <strong><em>transparency slider setting</em></strong> controls the visibility
116 of features rendered below other features. Reducing the transparency
117 will mean that features at the top of the list can obscure features
118 lower down, and increasing it allows the user to 'see through' the
119 upper layers of a set of features.
122 <strong><em>You can save all features, with their
123 current colours and visibility in a Jalview format file. </em></strong>